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3en8

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of NTF-2 like protein of unknown function (YP_553245.1) from BURKHOLDERIA XENOVORANS LB400 at 1.85 A resolution. To be published
    Site JCSG
    PDB Id 3en8 Target Id 390635
    Molecular Characteristics
    Source Burkholderia xenovorans lb400
    Alias Ids TPS14591,YP_553245.1, 3.10.450.50, 85681 Molecular Weight 14614.42 Da.
    Residues 127 Isoelectric Point 5.29
    Sequence mreekirealnahwqasaagdfdaehdiydddaicdypqsgerilgrmnlqalrshhpgkpagfevrri qgegnlwiteysisyngrpaytvsimefrngkvvhetqyfsdpfeapgwrsqwvqqig
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.85 Rfree 0.228
    Matthews' coefficent 2.90 Rfactor 0.185
    Waters 129 Solvent Content 57.53

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3en8
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    H Van Den Bedem, A Dhanik, JC Latombe - Section D: Biological , 2009 - scripts.iucr.org
     
    3. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     
    4. Structural and Functional Study of Yer067w, a New Protein Involved in Yeast Metabolism Control and Drug Resistance
    T Domitrovic, G Kozlov, JCG Freire, CA Masuda - PloS one, 2010 - dx.plos.org
     

    Protein Summary

    Gene Bxe_B2092 from BURKHOLDERIA XENOVORANS LB400 encodes the YP_553245 protein.

    Pre-SCOP classifies 3en8 in the alpha+beta class, NTF2-like superfamily. 3en8 is structurally similar to ketosteroid isomerases (PDB code: 1qjg; rmsd 2.1A for 112 aligned Ca, 20% seq id; DALI Z-scr=15) and steroid delta-isomerases (PDB code: 8cho; rmsd 2.7A for 113 sligned Ca, 21% seq id; DALI Z-scr=15). Their structure superposition with 3en8 is shown below.

    super_1qjg_8cho.png

    Fig. 1. Superposition of 3en8 (green) with 1qjg (cyan) and 8cho (pink).
     

    3en8 assembles as a monomer in the crystallographic asymmetric unit and the likely biological molecule is a dimer. 1qjg and 8cho also form biological dimers; however, their oligomerization modes are different from 3en8 as shown in Fig 3.

    super_dimer_1qjg_8cho.png

    Fig. 3. Superposition of the biological molecules of 3en8 (green) with that of 1qjg (cyan) and 8cho (pale cyan). The dimer formation of 3en8 is different from that of qjg and 8cho. (Dimer formations of 1qjg and 8cho are similar.)

     

    References:

    1.  Cho, H.S.,  Ha, N.C.,  Choi, G.,  Kim, H.J.,  Lee, D.,  Oh, K.S.,  Kim, K.S.,
    Lee, W.,  Choi, K.Y.,  Oh, B.H.  (1999) Crystal structure of
    delta(5)-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with
    equilenin settles the correct hydrogen bonding scheme for transition state
    stabilization.  J.Biol.Chem.   274: 32863-32868

     

    2. Cho, H.S.,  Choi, G.,  Choi, K.Y.,  Oh, B.H.   (1998) Crystal structure and
    enzyme mechanism of Delta 5-3-ketosteroid isomerase from Pseudomonas
    testosteroni.  Biochemistry   37: 8325-8330
     


     

    Ligand Summary

    A Ca++ ion and a PEG 600 fragment (PG4) were modeled based on crystallization condition. The Ca++ ion is not involved in the dimer interface, however, it's involved in crystal packing of the neighboring dimers as shown below.  

    ca1.png

    Fig. 1. Ca++ ion (yellow green sphere) interacts with Asp 32 (green, 1st left)- 31( green, 2nd left) and Asp 30 (grey, top right) -31 (grey, bottom right) of the symmetry mates and a HOH (red sphere).  

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